Hello, our lab (engineering dept.) has no expertise in NGS or bioinformatics. We are planning to send sludge samples for 16S sequencing on the MiSeq instrument. How long do you think it would take for an M.Sc student to learn about this assay and the tools to be used like Qiime or Mothur? Is it realistic or should we seek help from a bioinformatics group?
How long do you think it would take for an M.Sc student to learn about this assay and the tools to be used like Qiime or Mothur?
its really depends on the skills of your M.Sc student. If student as no programming skills, it can be a long process to understand 16S analysis pipeline. Someone with experience could probably have a pipeline running within a week. One important step that is usually neglected by students in the analysis process is the QC surrounding the analysis method.
In my opinion, the best strategy i think would be to have the pipeline developped by someone with experience and make the student run the pipeline and validate the results. After running the pipeline a couple of times, the student will learn and understand the pipeline steps and possible be able to update and improved the pipeline based on your 16S sequencing data.
Honestly? Probably a month of part-time work on the project if they have no prior experience. This includes learning how to use the command-line and submit jobs on a cluster. Someone with more experience would be able to do it faster. I actually recommend having the student do the analysis in either case – the skills payoff at the end of the day is definitely worth it.